MPs and peers have "rediscovered their collective balls" over the phone-hacking affair, the Speaker has told the Guardian. John Bercow calls for further reforms to strengthen parliament, including clearer sanctions against witnesses who refuse to attend, or deliberately mislead, select committees.

In a rare newspaper interview with the Guardian, Bercow reveals that parliamentary officials had been unclear about how to respond when Rupert Murdoch, chairman of News Corp, initially said he would not give evidence to the culture select committee .

"If the Murdochs had refused the warrant to attend, we would have been in an extremely awkward situation. I don't think there is much we could have done. There has been a complete ambiguity, a lack of clarity, an uncertainty about what our powers are."

Bercow says select committees should have enforceable powers to compel witnesses in British jurisdiction to attend, and not, as at present, "depend on a toxic blend of bad publicity and the entirely implausible threat of imprisonment.

"I don't think frankly it should be the Speaker on behalf of the house imprisoning a witness. We have got a creche in the parliamentary estate, but not so far as I know a cell."

He favours select committees requiring witnesses to give evidence on oath as a matter of course, with a clear punishment for making knowingly misleading statements. "Lying to a committee is a very grave abuse and there ought to be a clear punishment," he says. In calling for urgent action, he adds: "This is a case of striking while the iron is hot. The issue is here and now. Why not act on it? It should be set out in a modern way so we all know what powers we have got and witnesses know what powers they have got."

One option is to give parliament powers to fine witnesses who do not co-operate. But Bercow wants to see if there is all-party support for the criminal law to intervene against unco-operative witnesses, as well as an additional "sparingly used power" to call them to the bar of the Commons to apologise.

Senior News International executives have already been accused by the culture select committee of "collective amnesia", and this week it was alleged that James Murdoch misled parliament, a charge he has denied.

Bercow said he was "extremely angry and embarrassed" by the assault on Rupert Murdoch as he gave evidence this week, adding "it could have been acid and not shaving foam".

He adds: "In and immediately outside the committee room, the situation was a mess and that's why I decided straight away that there should be an independent expert investigation." The inquiry will look at the policing of high-profile witnesses, searches of the public, more thorough screening and the layout of the committee room so the public are seated further from the witness, possibly behind the chairman, as opposed to the witness.

"We simply cannot run the risk of this happening again," he says, praising Rupert Murdoch for continuing to give evidence.

Bercow also suggests other changes, including reform of the Commons' hours to match a typical working day, helping to make family life more compatible with politics. He says if businessmen can hold "power breakfasts" it should not be ruled out that select committees meet before 9am. "I don't see that this would shake the foundations of the constitution."

Since his election as Speaker, Bercow has been the subject of persistent sniping by some Conservative MPs and newspapers furious at what they regard as his bias to Labour, or his willingness to challenge tradition, including by discussing parliament's role in public life.

But some MPs have hailed him for giving them a platform to pursue the phone-hacking affair.

Bercow says: "Parliament has started to reassert itself. We have rediscovered our collective balls. I would not want to be smug or complacent. We are now out of intensive care, but we are still in the recovery unit. He expresses his frustration at the conduct of prime minister's questions saying: "I cannot think of any business that would put its worst product in the shop window and in some respects it's our worst product. I think the level of heckling, the extent of catcalling, the sheer decibel level, are not conducive to reasoned debate."

He admits "the Westminster beltway and political cognoscenti" disagree with him, but says he is willing to conduct opinion polls to see if, as he suspects, the general public side with him. "I think there are a lot of people at home who hear this kind of debate and think 'No' if we have disagreements in our family or at the dinner table we discuss things in a civilised way." He says: "I do not know if party leaders or whips, often the bastions of party tribalism, are willing to take this mission seriously."

He also ascribes parliament's revival to "a fantastic intake of 227 new MPs untainted by the past", a set of reforms passed at the end of the last parliament to rebalance the relationship between the executive and parliament, and his own willingness to call ministers to the Commons to answer emergency questions, so giving the Commons "greater urgency, topicality and relevance". Bercow has granted 60 urgent questions compared with the two granted by the previous Speaker Michael Martin, without complaint from ministers.